Testing and quantifying phylogenetic signals and homoplasy in morphometric data

Abstract.—The relationship between morphometrics and phylogenetic analysis has long been controversial. Here we pro-pose an approach that is based on mapping morphometric traits onto phylogenies derived from other data and thus avoids the pitfalls encountered by previous studies. This method treats shape as a single, multidimensional character. We propose a test for the presence of a phylogenetic signal in morphometric data, which simulates the null hypothesis of the complete absence of phylogenetic structure by permutation of the shape data among the terminal taxa. We also propose 2 measures of the fit of morphometric data to the phylogeny that are direct extensions of the consistency index and retention index used in traditional cladistics. We apply these methods to a small study of the evolution of wing shape in the Drosophila melanogaster subgroup, for which a very strongly supported phylogeny is available. This case study reveals a significant phylogenetic signal and a relatively low degree of homoplasy. Despite the low homoplasy, the shortest tree computed from landmark data on wing shape is inconsistent with the well-supported phylogenetic tree from molecular data, underscoring that mor-phometric data may not provide reliable information for inferring phylogeny. [Drosophilidae; geometric morphometrics; homoplasy; phylogeny; Procrustes superposition; shape; squared-change parsimony.] Understanding the evolution of organismal form i